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This is the development version of ELMER; for the stable release version, see ELMER.

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Bioconductor version: Development (3.20)

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Author: Tiago Chedraoui Silva [aut, cre], Lijing Yao [aut], Simon Coetzee [aut], Nicole Gull [ctb], Hui Shen [ctb], Peter Laird [ctb], Peggy Farnham [aut], Dechen Li [ctb], Benjamin Berman [aut]

Maintainer: Tiago Chedraoui Silva <tiagochst at>

Citation (from within R, enter citation("ELMER")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1 - ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles HTML R Script
11 - ELMER: Use case HTML R Script
2 - Introduction: Input data HTML R Script
3.1 - Data input - Creating MAE object HTML R Script
3.2 - Identifying differentially methylated probes HTML R Script
3.3 - Identifying putative probe-gene pairs HTML R Script
3.4 - Motif enrichment analysis on the selected probes HTML R Script
3.5 - Identifying regulatory TFs HTML R Script
3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way HTML R Script
4.1 - Scatter plots HTML R Script
4.2 - Schematic plots HTML R Script
4.3 - Motif enrichment plots HTML R Script
4.4 - Regulatory TF plots HTML R Script
4.5 - Heatmap plots HTML R Script
5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI HTML R Script
Reference Manual PDF


biocViews DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version 2.29.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.4.0),>= 2.9.3)
Imports GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks(>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer(>= 1.61.2), DelayedArray
System Requirements
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Suggests BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData
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Depends On Me
Imports Me TCGAWorkflow
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package ELMER_2.29.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ELMER_2.29.0.tgz
macOS Binary (arm64) ELMER_2.29.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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